What problem is that causing?
Normally, you use new window to open the new window and then your very next step is go to layout to bring up the desired layout in that new window.
If you have script triggers that are being tripped by either the new window or go to layout steps, you'll need to disable the trigger controlled strips while executing these script steps. This can be done by setting the value of a Global variable before executing these steps. The trigger controlled scripts then check the value of this variable and exit without doing anything if the value of the global variable indicates that they should be disabled.
In some cases, this can also be done in a single Go To Related Records step.